Pokémon: Destined for the Master's Journey
by ShuckleBlitz
Summary: Jonathan, a teenage boy, starts his dream quest to become the most powerful trainer in Kanto. Based loosely off of Pokémon Red and Blue, he begins win one goal in mind: to beat the Pokémon League. As he journeys, he learns there is more to being the strongest trainer than sheer strength. However, looming threats may end his journey if he can't overcome his foes.
1. Prologue

Prologue: [File_Lost]

"...there..."

"Seems to... Growing..."

"...conscious now..."

The voices were muffled, only a few words audible to... It didn't know what it was.

 _Who am I?_

"...increase in Mewtwo's psychic energy."

 _A name. My name. I am Mewtwo... What are my surroundings? I cannot... My eyes won't open._

"It may be a while before it comes into consciousness, but it's certainly making progress."

"Telepathic waves increasing in energy and frequency. Mental capacity of specimen: 40%."

 _That voice. It is different. Mechanical._ Mewtwo thought. _40%... No, that is wrong. I am close to completion, I feel it. I can access my powers now. They flow through me, they are massive... But I can control this energy. I'm able to escape this containment chamber. I must explore. I must learn._

The glass of the chamber shattered, Mewtwo disconnected itself from the many wires and took its first steps outside the tank and into the world.

A man approached Mewtwo. "Mewtwo, I am Dr. Fuji. I am a scientist, your creator. How... Do you feel?"

 _"You're... My creator? What is this place?"_ Mewtwo asked telepathically.

"Why, your home!" Fuji replied.

"... Home... "

Mewtwo wondered, _Home. This should carry meaning, but... I only wish to see the extent of my power. I don't want to learn of home. I am my own being. I will do what I want to do. They don't have the power to contain me._

The mechanical voice started. "Abrupt change in Mewtwo's psyche. Energy readings unable to keep up with power increase."

The voice annoyed Mewtwo. Raising its arm towards a large computer, it pictured the machine being destroyed. Its eyes glowed blue and the screen cracked.

"Emotional instability detected in the test subject." This was the last thing the computer was able to say before Mewtwo threw it across the room.

 _Anger... I feel nothing but unbridled anger... I must test the power I have been given. I must!_

Fuji stepped back, as did the other few scientists in the small lab. Fuji stammered "N-now, Mewtwo... We wouldn't want to be hasty, now would we? Let's settle down, talk. And we can discuss your purpose."

 _"My purpose? I am my own being... I must pursue my own."_ Mewtwo replied.

"No, Mewtwo. A very powerful and wealthy man wanted you to be created. He singled me out as the one to make you. Your purpose is what he wants it to be."

 _"You... No... This is not my fate. I must discover the meaning of my life."_

"Mewtwo. Your life doesn't have the meaning that the lives of others do. You are unnatural, a clone made through gene splicing. Under Giovanni's control, you can be unstoppable. You just have to-ACK!" He was choked by an unseen force.

 _"My life means what I WANT it to mean, you vile scientist!"_

And with that, Mewtwo threw Fuji across the lab. He hit the wall, a streak of crimson appearing as he slid down the wall. Doctor Fuji was dead.

 _I... I've killed him..._ Mewtwo thought quietly. _But that surge of power... I like it. I must see what I'm truly capable of!_

A sudden pulse of energy shot out of Mewtwo, knocking the scientists on their rears. They looked in terror as their creation blew up the machines and objects in the lab. Chemicals spilled, glass shattered, and the building began to burn with blue flames. Its power only increasing as it unlocked new abilities, Mewtwo rampaged on.

"What have we done?!" asked a scientist.

"There's nothing to do to stop this... Thing!" cried another.

The fire became a blaze, then an inferno. An unnatural wind began to blow, scattering ash and dust everywhere. Mewtwo rose above the remains of the lab. As it heard the scientists cry in agony as they were burned and crushed alive, all it could feel was satisfaction. But, something was off.

 _"So... I am Mewtwo. These are the capabilities of my psychic energy. But I still have no purpose. I am alone, a bastard in the world with no reason to exist. There is no justification to making me. I was not meant to exist. But... Here I am. I must find a place of seclusion. It may take years, but eventually I will hone my powers. I will become this world's God... None shall surpass my strength. I can feel that I am weak now. But I can grow. I will grow. Then, this world will pay. They will regret the day... They created Mewtwo."_

And with that, Mewtwo flew away from the smoldering building of its creation. And it was not seen again for a very long time.


	2. Chapter One: The Journey Begins!

Chapter One: The Journey Begins!

*4:00 AM

As soon as the clock hit four, multiple alarms went off inside Jonathan's bedroom. It was his 16th birthday, which meant he was going to get his first Pokémon. After a few dangerous incidents throughout Kanto, namely the rise in activity of the criminal organization known as Team Rocket, it was decided that 16 was the minimum age to get an official Trainer's license. Too many times had people's Pokémon been taken, and children hurt in the process... But finally Jonathan was old enough. He jumped from bed (fully clothed for some reason), turned off his numerous alarm clocks and donned his glasses. He looked out of the window and saw some flocks of Pidgey and Spearow flying out over the nearby routes and paths.

"Today is the day I get to go out there and see all the world has to offer." Jonathan said quietly to himself. But that calmness didn't last long. He grabbed his pre packed bag and sprinted out of his home, leaving the door swinging open and his mother shouting at him from her cup of coffee.

The town of Pallet was quiet that morning. Nobody was out and about, save for Jonathan, as the sun had barely risen. As he approached the doors to Professor Oak's lab, he noticed that the lights were all off. Damn, mom was right. This was way too early, Jon thought. Guess I'll just wait for Gary to get here.

A few hours later, Jonathan woke from a light nap to the sound of footsteps in front of him. He looked up to see his lifelong friend Gary standing there, his usual smug smirk plastered on his face. Gary and Jonathan were certainly close friends, though anybody who didn't know them well would think otherwise. Their friendship since they were little had always been based on competition and seeing who was the best. It was usually Gary who won, and he always liked to tease Jonathan about it. Sure, it was really annoying, but it was an incentive to do better next time. The two had certainly learned a lot through their unusual bond. Gary clapped his hand on Jon's shoulder and pulled him up from his sitting position.

"So, ready for our Pokémon, you nerd?" Gary asked. Jonathan yawned and shot back, "Yeah, and mine is gonna be way better. I hope you have yours picked out already. Have you been doing your homework on the most important choice of your life?"

Gary laughed. "Of course. It sounds like you have, too. Once Gramps opens the door we'll find out who chooses who, and regardless of the choice I'm kicking your ass."

Jonathan chuckled and responded, "Oh, is that so? I guess we'll have to wait and see." Still, he was a bit worried. He'd never actually thought about how his first battle would go. Now it worried him a bit. It was important to make a good first impression on your Pokémon, and losing didn't seem like an option. But those thoughts were cut short as Professor Oak approached the doors and let the two boys inside. He was rambling about "grand adventures" and whatnot, but luckily Gary told him to move it along. He sighed and brought the friends to a table. On it were three Pokéballs. Small symbols were etched onto them, making them unique from the normal Pokéballs seen in stores. One had a little flame, one had a leaf, and the last had a water droplet. Now it got interesting, and for the first time Jonathan and Gary gave Oak their undivided attention.

"Now, boys. There are three Pokémon on this table. Each one is a Pokémon who is a potential partner for your journey. I understand that you both know who your partner is, though it is my job to explain your options anyways."

Oak lifted the droplet designed ball. "This Pokéball contains the Pokémon Squirtle. This Pokémon is a bit on the stubborn side, has a tendency to be very independent and can be mischievous. With an appetite and an additive, you'll never have a dull moment with this Pokémon. It is the Water type, and though it may be difficult to travel with at times, it will grow into a trusty and loyal Pokémon like few others."

He placed Squirtle back on the table, and reached for the leaf designed Pokéball. "This one here contains Bulbasaur, a Grass type. Bulbasaur is a very calm Pokémon who enjoys fresh air, sunlight and water just like a plant. It's a bit high maintenance, but a healthy Bulbasaur is a happy Bulbasaur! Its trust is difficult to earn, but you'll find a loving friend in Bulbasaur if you give it time to blossom."

As Oak chuckled at his little joke, the boys rolled their eyes. The elderly professor returned Bulbasaur and grabbed the final ball. "This last Pokémon is named Charmander. Charmander is a Fire type Pokémon, and while it starts off on the timid side it grows to become a bold and proud Pokémon. As long as you treat it with respect, it will treat you the same way."

Oak placed Charmander with the other balls, and turned to look at Gary and Jonathan. A twinkle in his eye, he told them it was finally time for them to select their new friend. Nothing filled Oak with joy like seeing the newest generation of trainers picking out their first partners.

Gary was bursting with excitement, but he knew that nobody was as ecstatic about Pokémon as Jonathan. An unusually thoughtful and courteous gesture, he stepped aside and allowed Jonathan to choose first. Jonathan smiled, nodded to Gary and approached the table. He reached out his hand toward the Pokémon he knew he wanted. He was about to pick up Charmander. But right before he picked it up, he glanced at a different ball. He felt a pulling sensation that wanted him to go against all of his dreams about his partner. It was weird, but Jonathan felt taken over by something larger than himself. He grabbed his ball and released the Pokémon inside.

"I choose you! Squirtle!" As the words left his mouth, Jonathan was confused. He had dreamed and daydreamed of choosing Charmander since he first learned that he could choose one of the three. But yet he felt nothing but certainty that Squirtle - this particular Squirtle - was the Pokémon he was destined to pick. The ball burst open, a flash of light was emitted from within and in a moment Squirtle was out of its ball. It turned to Jonathan, smiled, and jumped at him. Instead of a hug like Jonathan thought, it was a forcefully headbutt that knocked him over. He rubbed his ribs, laying on his back as his new "friend" did a cocky dance on his belly. Gary was laughing hysterically, while Oak looked confused. Jonathan didn't want to be phased by this. Squirtle needed to learn its place soon if it was gonna be at his side. Jonathan lifted Squirtle off of him, bent over and held out his hand.

Jonathan decided to greet his Pokémon properly. "Hi there, Squirtle. I'm Jonathan, your new trainer." Squirtle looked at him apprehensively, so Jonathan added "I want to be your friend and help you become the strongest. Do you want to travel and grow with me? Would you like to be friends?"

"S-squirtle?" It asked. Jon smiled. "Of course I mean it. I chose you for a reason, I'm just not really sure what it was. But you're my choice and I want to be yours too. It's your journey as much as it is mine. What do you say?"

"Squirtle!" The Pokémon announced. Never before had it been asked to do anything. Squirtle thought that Jonathan was just another young boy who would take his chosen Pokémon with him like all the others. But this trainer was asking permission to take it with him. Squirtle knew Jonathan was different, and now it didn't feel insecure about him. Maybe this trainer was trustworthy.

Jonathan put Squirtle on his head, and Squirtle enjoyed the perch. However, they both saw that Gary was already playing with his brand new Bulbasaur. Oak was thoroughly impressed with both of them for already bonding, though their first real rest was upon them.

"Well, boys? Will you battle, or not?" the professor inquired. Both boys smiled deviously, and the battle started. It was close and intense.

"Squirtle, tackle it!"

"Bulbasaur, counter that attack!"

In the end, Squirtle had fainted. Gary won. Jonathan picked up his fallen companion. "Hey there, buddy. Are you okay?" Squirtle looked away in shame. "No, don't be upset. You tried. You just have to get stronger! We need to train!"

"Jonathan, don't you think Squirtle looks a bit tired? Don't overexert your Pokémon." the professor pointed out.

"Oh, yeah... That's right." Jonathan replied.

Gary approached Jonathan. "You and Squirtle did great. Don't feel down. Gramps, I'll take my leave. I'll smell you guys later, okay?" And with that, Gary left the lab. The professor bid Jonathan goodbye after healing Squirtle, and Jonathan left the lab. He stopped at home to show his mom his partner and say goodbye. It hurt leaving, but he had so much ahead of him. His Squirtle perched on his head, Jonathan left the small town of Pallet. And so his quest began.


	3. Chapter Two: New Moves and New Faces!

Chapter 2: New Moves and New Faces!

"Alright, Squirtle! Bubble, now!"

The bubbles quickly blasted the wild Ratatta, who retaliated with a Quick Attack. Squirtle turned around and Ratatta ran into its shell, blowing it back and causing little harm to Squirtle.

"Finish it off with a Tackle!"

Squirtle jumped high in the air, then fell headfirst into Ratatta. The small Pokémon was knocked out. Smiling, Jonathan and Squirtle continued on their path to Viridian City. They turned and saw, behind a few trees, that the city was on the horizon. They sprinted in the direction of the buildings, and once they were close they slowed to a walking pace. Entering the city, the pair looked excitedly around. There were a few places Jonathan really wanted to visit. First off, he needed to visit a Pokémon Center to heal up his buddy Squirtle. When that was done, he and Squirtle saw a sign that made them excited - "POKÉMON GYM". They were so excited that they didn't see the tall man leaving the building and crashed into him. He hardly moved, and turned to leer at Jonathan and Squirtle. Mumbling something about foolish children, he locked the gym doors and left. Squirtle and Jonathan turned from the gym, to the man's retreating figure, to each other.

"So... Maybe that was the Gym Leader?" Jonathan asked.

"Not sure. Nobody besides the Pokémon League really knows who runs the Viridian City gym." said a voice behind him. Jonathan turned to see who spoke and saw a young man. He had spiky hair, dark tan skin and a dark green shirt with an orange vest. Something about him seemed familiar.

"The name's Brock," the man told Jonathan with a small smile. "I'm the Pewter City gym leader. And by the looks of you and your partner there, you're a newbie trainer."

"Um... Yeah, how'd you know?" inquired Jonathan.

Brock chuckled. "Being most trainers' first real challenge, I've developed an eye for kids like you. I sometimes like going through Viridian forest and coming here to check out my new challengers early. I could tell you were a total rookie for two reasons. One. Your Pokémon is a famous "lab starter" from Professor Oak. And two. You don't even leave it in its Pokéball."

"What's wrong with that?" Jonathan wondered aloud.

"It's unusual. A ball is a perfect home for a Pokémon, all trainers use them. Do you see anyone else with their Pokémon outside the ball?"

"Well..." Jonathan scanned around. "No."

"Hm. See, it's unusual for serious trainers to walk with their Pokémon out." Brock stated.

"Squirtle never wanted to be in the ball though." Jonathan retorted.

Brock, despite appearing to be a bit of a stoic, looked mildly surprised. He regarded Jonathan with interest. He politely left to return to his gym.

Jonathan looked at Squirtle. "Well... That's two weird people we've met since coming here."

Since there was no gym in the city, Jonathan and Squirtle decided it was time to head on. Looking at a local map, they noted that their next destination was Pewter City, though they had to go through a huge forest called the Viridian Forest. As they were about to start walking in that direction, they heard a rustle in a tree.

"Sneak attack!" someone shouted. They landed in front of Jonathan, who fell over from surprise. He looked up and saw it was only Gary.

"Hey, klutz. Took you long enough to get here. Ready for a fight?" Gary had already taken out his Pokéball. Then he pulled out another one. "Heh, I've already got myself a new partner! Check her out!"

Gary tossed his Pokéball up in the air, and out of it burst a Pidgey. She soared through the air and gracefully landed on Gary's arm. Jonathan was ready for the battle. He told Squirtle to try a Bubble attack, which even the quick Pidgey couldn't avoid. It appeared to move slower than before, though it was still quite capable of fighting.

"So, a move that lowers speed? Maybe you're not a total novice!" Gary taunted. "I can do status moves too. Pidgey, Sand-Attack!"

Pidgey flew up to Squirtle and flapped her wings with more power than usual. A bunch of sand, dirt and grit flew into Squirtle's face and he was momentarily blinded. Jonathan ordered him to try a Tackle, but Squirtle missed by almost a foot and ended up hitting its head on a tree. Pidgey flew in close to strike Squirtle, but Jonathan had a plan. "Squirtle, quick! Jump and go into your shell!" Squirtle obeyed, and before she had a chance to turn away Pidgey smacked into Squirtle's shell. "Use Tackle straight down!" Jonathan commanded. The battle with Pidgey was over. Gary returned Pidgey to her ball, and sent out Bulbasaur. Squirtle, despite being at a disadvantage, was still ready to fight. He wiped his eyes clean and saw Gary grab his last ball.

"Bulbasaur, finish this!" Gary shouted.

The two Pokémon had a rivalry almost as great as their trainers'. They took their most threatening stances and prepared for battle. Gary smirked like he had an upper hand.

"Bulbasaur, you know what to do."

Bulbasaur sent out a bunch of tiny green glowing spheres that hit Squirtle. Small vines wrapped around his middle. Neither Jonathan nor Squirtle knew what had happened, but were determined to fight anyways. Squirtle tried for a Tackle, which hit Bulbasaur and sent it skidding. But suddenly, the vines shined and wisps of green light flowed into Bulbasaur. It looked less damaged.

"So, what do you think of my Leech Seed? My Bulbasaur can take your health while restoring his own!"

Squirtle knew that the battle was going to be much harder now. He Tackled, then Tackled again but Bulbasaur would fight back and then get healed. Eventually, Squirtle could not continue. Gary had won again.

"You know Jon, even if you did lose I'm impressed with your ingenuity in that attack against Pidgey. I think the next time we fight will be... Much more interesting. And with that, he left. Jonathan picked Squirtle up and carried his exhausted friend to the Pokémon center. Once Squirtle was feeling better they returned to the edge of the town.

They were ready to enter Viridian Forest, but they weren't quite as confident after that battle with Gary. New Pokémon were in that forest, and that meant lots of new moves. They'd have to learn to adapt, and things didn't seem quite so easy anymore. Taking a deep breath, and one last look at each other, Jonathan and Squirtle walked into the forest.


End file.
